Package | Description |
---|---|
com.compomics.util.experiment.identification.amino_acid_tags.matchers |
Tag matching classes.
|
com.compomics.util.experiment.identification.protein_inference |
Classes related to protein inference.
|
com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
|
com.compomics.util.experiment.identification.protein_inference.proteintree |
Protein sequence database indexing classes.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
TagMatcher.buildPeptides(String accession,
String sequence,
ArrayList<SequenceSegment> nTermPossibleSequences,
String seedSequence,
ArrayList<SequenceSegment> cTermPossibleSequences,
HashMap<Integer,ArrayList<ModificationMatch>> modificationsAtIndex,
int mutationsAtIndex)
Builds the possible peptides based on the given terminal segments and the
seed sequence.
|
ArrayList<PeptideProteinMapping> |
TagMatcher.getPeptideMatches(Tag tag,
String accession,
String sequence,
Integer tagIndex,
Integer componentIndex,
double massTolerance)
Returns the possible peptides which can be created on this sequence
indexed by their start index.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
PeptideMapper.getProteinMapping(String peptideSequence,
SequenceMatchingPreferences proteinInferencePreferences)
Returns the protein mapping in the FASTA file loaded in the sequence
factory for the given peptide sequence in a map: peptide sequence found
in the FASTA file | protein accession | list of indexes of the peptide
sequence on the protein sequence.
|
ArrayList<PeptideProteinMapping> |
PeptideMapper.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
ArrayList<PeptideProteinMapping> |
PeptideMapper.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
Returns the protein mappings for the given peptide sequence.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<String,HashMap<String,ArrayList<Integer>>> |
PeptideProteinMapping.getPeptideProteinIndexesMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
Returns a map made from the given mappings containing the indexes of the
peptides in the protein sequences indexed by peptide sequence and protein
accession.
|
static HashMap<String,HashSet<String>> |
PeptideProteinMapping.getPeptideProteinMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
Returns a map made from the given mappings containing protein accessions
for every peptide sequence.
|
static Collection<Peptide> |
PeptideProteinMapping.getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings,
SequenceMatchingPreferences sequenceMatchingPreferences)
Aggregates the given mapping into a list of peptides.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(String peptide,
SequenceMatchingPreferences seqMatchPref)
Main method for mapping a peptide with all variants against all
registered proteins in the experiment.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences)
Mapping tags against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
Mapping tags against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithoutVariants(String peptide,
SequenceMatchingPreferences seqMatchPref,
int indexPart)
Exact mapping peptides against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithoutVariants(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
int indexPart)
Mapping tags against proteome without variants.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithVariants(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
int indexPart)
Mapping tags against proteome with variants.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithVariantsGeneric(String peptide,
SequenceMatchingPreferences seqMatchPref,
int indexPart)
Variant tolerant mapping peptides against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithVariantsSpecific(String peptide,
SequenceMatchingPreferences seqMatchPref,
int indexPart)
Variant tolerant mapping peptides against the proteome.
|
Modifier and Type | Method and Description |
---|---|
boolean |
FMIndex.checkPTMPattern(PeptideProteinMapping peptideProteinMapping)
Checking if peptide-protein should be discarded due to pattern PTM conflict.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
Node.getProteinMapping(AminoAcidSequence query,
String currentSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
ArrayList<PeptideProteinMapping> |
ProteinTree.getProteinMapping(String peptideSequence,
SequenceMatchingPreferences proteinInferencePreferences) |
ArrayList<PeptideProteinMapping> |
ProteinTree.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences) |
ArrayList<PeptideProteinMapping> |
ProteinTree.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance) |
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